BN1737 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 7.9278e-06 2.3372e-04
Layer 3 1.8750e-05 7.6669e-04
Layer 2 6.2854e-05 2.5825e-03
Layer 6 1.8119e-04 8.3328e-03
Layer 5 4.3930e-04 1.8856e-03
WM 1.4136e-01 2.5064e-01
Layer 1 9.9487e-01 5.3878e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
NDFIP1 Expression Distribution
Gene Specificity Score (GSS)
NDFIP1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
NDFIP1 Layer 4 2.5000 0.7756
RAB6B Layer 5 2.4883 0.7725
PRKAR1B Layer 4 2.6660 0.7708
MEF2C Layer 4 3.0312 0.7706
NSF Layer 5 2.4785 0.7694
SPTAN1 Layer 4 2.5273 0.7680
SEZ6L2 Layer 4 2.9727 0.7678
LMO4 Layer 4 2.7969 0.7667
SV2A Layer 4 2.6660 0.7662
TAGLN3 Layer 4 2.6836 0.7660
ARL6IP1 Layer 4 2.4668 0.7659
B4GAT1 Layer 4 2.6016 0.7658
ATP2B2 Layer 4 3.0723 0.7648
RAB3A Layer 3 2.4883 0.7616
NAPB Layer 5 2.4395 0.7615
PPP2R1A Layer 5 2.3438 0.7588
STXBP1 Layer 4 2.6484 0.7587
MAPK8IP2 Layer 4 3.0918 0.7565
INA Layer 3 2.7793 0.7561
EEF1A2 Layer 4 2.5508 0.7554
CALY Layer 3 2.6074 0.7552
MDH1 Layer 4 2.4727 0.7548
ATP6V0A1 Layer 5 2.4727 0.7548
PREPL Layer 5 2.4336 0.7540
SYNGR1 Layer 5 2.9932 0.7537
SNCA Layer 5 2.6543 0.7534
GNG3 Layer 5 2.5898 0.7532
KLHDC3 Layer 5 2.5117 0.7521
SYN1 Layer 5 2.5840 0.7520
GABRG2 Layer 4 3.1934 0.7520
BEX1 Layer 2 2.5566 0.7514
GRIN1 Layer 4 2.7012 0.7511
FAIM2 Layer 5 2.3438 0.7508
SNCB Layer 4 2.6426 0.7503
SERPINI1 Layer 4 2.8281 0.7500
DYNLRB1 Layer 5 2.2900 0.7496
TOMM20 Layer 4 2.3965 0.7494
GABRA1 Layer 4 2.9277 0.7493
FXYD7 Layer 4 2.5664 0.7492
MAPK10 Layer 4 2.5117 0.7482
FXYD6 Layer 4 2.4668 0.7482
ATP1A1 Layer 4 2.8457 0.7481
TLE5 Layer 4 2.3398 0.7463
SOD1 Layer 4 2.1055 0.7460
SYP Layer 4 2.4082 0.7459
ATP6V0D1 Layer 5 2.4502 0.7448
RGS4 Layer 4 2.7188 0.7442
CYFIP2 Layer 4 2.5000 0.7440
CABP1 Layer 4 2.7852 0.7440
RUNDC3A Layer 4 2.8770 0.7438

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1737
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1737_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1737/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1737/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1737/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1737/report/PD/BN1737_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1737/report/PD/BN1737_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 06:19:07
  • Number of Processes: 10
  • Spending Time: 0h 3m